MK has Low-Godly as a ghost doesn't he? At least, according to the profile, he has Mid normally and his ghost form needs to absorb life from a target to recreate a body (Cloud resists Life Manip but needs to be aproved in CRT to be on his profile). I may be missing something, but, it has that caveat. Cloud can kill ghosts and souls, he explicitly destroyed Sephiroth's spirit in the original game and he can Hax ghosts and spirits as well. If I am getting it right (being honest here, let me know if I am wrong) even if not negated, the limitations of Low-Godly are still the destruction of your soul, correct?
I think that's precisely the issue, everything is too vague regarding Sephiroth now and he's pulling crazy nonsense that had absolutely no place nor mention before in the narrative of VII, Time Travel, Fate, Timelines, a Primordial Dimension, coexisting alternate counterparts, so who's to say that Sephiroth now exists as a constant of chaos challenging the order within the universe that can't be erased by the flow of time and destiny or some of that pretentious yadda yadda Squeenix loves, the same way that Cloud could have fell short again, who knows?. While I don't disagree that Sephiroth's final words may be being used to tie into his new role in the Remake, but there is no information as to when he Time Travelled (was it at the end of AC or with DoC's stinger with Genesis' criptic message? for example) or how is he doing it exactly, we can simply guess and assume without real evidence until next chapters reveal what's the deal.